# Tools for Environmental Analyses, Ecotoxicology and Various R Functions

## Documentation for package ‘HelpersMG’ version 6.6

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F I L M N O P Q R S T U W

HelpersMG-package | Tools for Environmental Analyses, Ecotoxicology and Various R Functions

## -- A --

addS3Class | Add a S3 class to an object.
as.mcmc.mcmcComposite | Extract mcmc object from a mcmcComposite object
as.parameters | Extract parameters from mcmcComposite object
as.quantiles | Extract quantile distribution from mcmcComposite object
asc | Return the codes (in UTF-8) of a string

## -- B --

barplot_errbar | Plot a barplot graph with error bar on y

## -- C --

cArrows | Draw curved lines with arrowhead
ChangeCoordinate | Return a value in a changed coordinate
char | Return the characters defined by the codes
compare | Run a shiny application for basic functions of comparison
compare_AIC | Compares the AIC of several outputs
compare_AICc | Compares the AICc of several outputs
compare_BIC | Compares the BIC of several outputs
contingencyTable.compare | Contingency table comparison using Akaike weight
convert.tz | Convert one Date-Time from one timezone to another
cutter | Distribution of the fitted distribution without cut.

## -- D --

d | Write an ASCII Representation of a vector object
dbeta_new | Density for the Beta distributions.
dcutter | Distribution of the fitted distribution without cut.
dggamma | Generalized gamma distribution.
DIx | Return an index of quantitative asymmetry and complexity named Developmental Instability Index (DIx)
dnbinom_new | Random numbers for the negative binomial distribution.
dSnbinom | Distribution of the sum independent negative binomial random variables.
duplicated_packages | List the duplicated packages with their locations

## -- E --

ellipse | Plot an ellipse
ExtractAIC.glm | Return AIC, AICc or BIC from a glm object

## -- F --

fitdistrquantiles | Parameters of beta, normal or gamma distribution based on quantiles.
flexit | Return the flexit
FormatCompareAIC | Format data to be used with compare_AIC()
format_ncdf | Return an array with ncdf data
from_min_max | Distribution from minimum and maximum

## -- I --

iCutter | Run a shiny application to fit bone section
IC_clean_data | Clean the dataframe before to be used with IC_threshold_matrix
IC_correlation_simplify | Simplify the correlation matrix
IC_threshold_matrix | Calculate correlation matrix
index.periodic | Estimate indices in periodic timeseries based on anchored minimum and maximum
ind_long_lat | Return or the index in ncdf object from lat/longitude or inverse
inside | Search a string within files of a folder
invlogit | Return the inverse logit

## -- L --

LD50 | Estimate the parameters that best describe LD50
LD50_MHmcmc | Metropolis-Hastings algorithm for LD50
LD50_MHmcmc_p | Generates set of parameters to be used with LD50_MHmcmc()
list.packages | List the installed packages with their locations
local.search | Return path of file searched for in local disk based on its file name
logit | Return the logit
logLik.compareAIC | Return Log Likelihood generated by FormatCompareAIC
logLik.cutter | Return log likelihood of a cutter fitted model
logLik.LD50 | Return Log Likelihood of a fit generated by LD50

## -- M --

merge.mcmcComposite | Merge two mcmcComposite results
MHalgoGen | Monte-Carlo Markov-chain with Metropolis-Hastings algorithm
minmax.periodic | Search for minimum and maximum indices in periodic timeseries
modeled.hist | Return the theoretical value for the histogram bar
modifyVector | Modifies Elements of a Vector
moon.info | Moon phase based on a date
MovingWindow | Return a moving average of a vector.

## -- N --

NagelkerkeScaledR2 | Return the scaled R2 defined by Nagelkerke (1991)
newcompassRose | Display a compass rose
newmap.scale | Add Scale to Existing Unprojected Map

## -- O --

openwd | Open a finder window with current working directory in MacOS X and windows

## -- P --

pggamma | Generalized gamma distribution.
plot.cutter | Plot results of cutter that best describe distribution
plot.IconoCorel | Clean the dataframe before to be used with IC_threshold_matrix
plot.LD50 | Plot results of LD50() that best describe LD50
plot.mcmcComposite | Plot the result of a mcmcComposite object
plot.PriorsmcmcComposite | Plot a prior defined with setPriors function
plot_add | Add a plot to a previous one
plot_errbar | Plot a xy graph with error bar on x and/or y
predict.LD50 | Estimate survival according to doses
print.cutter | Print results of cutter that best describe distribution
pSnbinom | Distribution of the sum independent negative binomial random variables.

## -- Q --

qggamma | Generalized gamma distribution.
qSnbinom | Distribution of the sum independent negative binomial random variables.
qvlmer | Quasi Variances for lmer Model Coefficients

## -- R --

r2norm | Random generation for Gaussian distributions different at left and right
RandomFromHessianOrMCMC | Random numbers based on Hessian matrix or MCMC
rcutter | Random values of unobserved values of cut distribution.
read_folder | Read files present in a folder and creates a list with the content of these files
RectangleRegression | Return parameters of rectangle regression
rggamma | Generalized gamma distribution.
rmnorm | Generate random numbers from the multivariate normal distribution
RM_add | Create a results managment or add a value in a results managment to an object
RM_delete | Delete a results managment or a result within a results managment from an object
RM_duplicate | Duplicate a results managment within an object.
RM_get | Get a value in a results managment to an object
RM_list | Return the list of results managment of an object.
rnbinom_new | Random numbers for the negative binomial distribution.
rSnbinom | Distribution of the sum independent negative binomial random variables.

## -- S --

ScalePreviousPlot | Return the scale of the previous plot
SEfromHessian | Standard error of parameters based on Hessian matrix
series.compare | Data series comparison using Akaike weight
setPriors | Set priors for MHalgoGen()
show_name | Show the name of a point
similar | Test if two vectors contains the same elements independently of their order
specify_decimal | Return a number as character with specified number of decimals
summary.mcmcComposite | Summarize the result of a mcmcComposite object
sun.info | Estimate the time of sunrise and sunset according to longitude, latitude and date
symbol.Female | Plot a female symbol in the plotting region
symbol.Male | Plot a male symbol in the plotting region
symmetricize | Make a matrix symmetric

## -- T --

tide.info | Annual tide calendar for one particular location
tnirp | Read an ASCII text representation of a named or not vector object

## -- U --

universalmclapply | Run the function FUN on X using parallel computing

## -- W --

wget | Download a file from internet and save it locally